Hi DJ N,
Do you run any dew control on your scope?
My graphs on my HEQ5 look similar when the guidescope starts to dew up. Like you my main image looks fine, but the graph doesn't look so great. If it dews up real bad, eventually PHD loses the star.
Does it guide like this from the start or takes a few mins before it gets to this stage?
Also have you setup a PEC profile?
Your DEC is up and down in a sort of pattern, so a PEC profile may help you (or not). There is a nice tool that will take a PHD log file and display some graphs for PEC training, which should help you determine if it is periodic error or something else.
Conveniantly, i can not remeber its name or where i got it from. I believe there is a link on Stark-labs website somewhere.
The only other thing i can think of is that maybe your mount is not levelled, but im guessing you have made sure it is as level as you can get it.
Finally, you can always try drift aligning altitude as well, won't hurt to check.
-edit-
I learn't to read, removed my stuff up.
-edit 2-
Found a month old image of PHD i took, this was with a QHY5 on an Orion ST80 guidescope. Possibly try the settings i used (RA hys/agr) and max DEC
http://core-au.net/astro/phd.png
(disregard terrible stars, thats not a tracking problem, main scope had a "problem")